Incorrect codon files generated by scikit-ribo-build for mm10 #7
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Yes, we are aware of some issues when processing higher eukaryotic genomes
that seems to be related to the way that UTRs and spliced transcripts are
processed by the libraries we are using. We are hoping to address this in
the near future, but unfortunately, we do not have a specific timeline
available at this time. Please keep an eye on the github pages for a future
announcement.
Thank you,
Mike
…On Thu, Jul 26, 2018 at 1:41 PM nabeel1990 ***@***.***> wrote:
I have been trying to use scikit-ribo on mouse ESC Ribo-Seq data but the
output files generated from scikit-ribo-build do no correctly parse the
given input GFF file. I am using the mm10_knownGene GFF file as input with
genome file obtained from
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/.
Specifically, there is inaccurate assignment of codons of transcripts.
For example, for gene uc008cjg.1, the start codon is at chr17:
35916361-35916363 while the in the files mm10.codons.df and
mm10.codons.bed, this chromosome location is at codon 2
$ cat mm10.codons.bed | grep 'uc008cjg.1' | head -12
chr17 35916390 35916393 uc008cjg.1 -8 - CGG
chr17 35916387 35916390 uc008cjg.1 -7 - CAG
chr17 35916384 35916387 uc008cjg.1 -6 - GCC
chr17 35916381 35916384 uc008cjg.1 -5 - GTA
chr17 35916378 35916381 uc008cjg.1 -4 - CGT
chr17 35916375 35916378 uc008cjg.1 -3 - CCG
chr17 35916372 35916375 uc008cjg.1 -2 - GTG
chr17 35916369 35916372 uc008cjg.1 -1 - TGC
chr17 35916366 35916369 uc008cjg.1 0 - GTC
chr17 35916363 35916366 uc008cjg.1 1 - AAG
chr17 35916360 35916363 uc008cjg.1 2 - ATG
chr17 35916357 35916360 uc008cjg.1 3 - GCT
Another example where the codon assignments are entirely different from
the reference is uc007vnb.1. The start codon is at chr15:37003817-37003820
but the codon file has very different annotations.
$cat mm10.codons.bed | grep 'uc007vnb.1' | head -20
chr15 37007423 37007426 uc007vnb.1 -8 - CCG
chr15 37007420 37007423 uc007vnb.1 -7 - CAG
chr15 37007417 37007420 uc007vnb.1 -6 - GAA
chr15 37007414 37007417 uc007vnb.1 -5 - GGT
chr15 37007411 37007414 uc007vnb.1 -4 - GAG
chr15 37007408 37007411 uc007vnb.1 -3 - GGG
chr15 37007405 37007408 uc007vnb.1 -2 - CGG
chr15 37007402 37007405 uc007vnb.1 -1 - GAC
chr15 37007399 37007402 uc007vnb.1 0 - CGC
chr15 37007396 37007399 uc007vnb.1 1 - GCG
chr15 37007393 37007396 uc007vnb.1 2 - GGC
chr15 37007390 37007393 uc007vnb.1 3 - AAG
Assuming that codon 0 is the start codon in this file, I found that only
3380(7%) of 46355 transcripts have ATG as start codon
cat mm10.codons.bed | awk '{if($5==0)print $5,$7}' | sort | uniq -c
727 0 AAA
436 0 AAC
748 0 AAG
376 0 AAT
686 0 ACA
473 0 ACC
295 0 ACG
854 0 ACT
1768 0 AGA
1212 0 AGC
1207 0 AGG
1724 0 AGT
377 0 ATA
522 0 ATC
**3380 0 ATG**
704 0 ATT
228 0 CAA
377 0 CAC
493 0 CAG
167 0 CAT
400 0 CCA
569 0 CCC
399 0 CCG
477 0 CCT
188 0 CGA
602 0 CGC
637 0 CGG
136 0 CGT
202 0 CTA
831 0 CTC
625 0 CTG
594 0 CTT
990 0 GAA
779 0 GAC
1888 0 GAG
585 0 GAT
921 0 GCA
1177 0 GCC
1318 0 GCG
928 0 GCT
1856 0 GGA
1691 0 GGC
2329 0 GGG
1037 0 GGT
523 0 GTA
1015 0 GTC
1304 0 GTG
916 0 GTT
90 0 TAA
88 0 TAC
184 0 TAG
115 0 TAT
284 0 TCA
401 0 TCC
162 0 TCG
386 0 TCT
285 0 TGA
392 0 TGC
460 0 TGG
270 0 TGT
155 0 TTA
506 0 TTC
274 0 TTG
632 0 TTT
I hope this bug can be fixed so that scikit-ribo can be run on mm10 data.
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I have been trying to use scikit-ribo on mouse ESC Ribo-Seq data but the output files generated from scikit-ribo-build do no correctly parse the given input GFF file. I am using the mm10_knownGene GFF file as input with genome file obtained from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/.
Specifically, there is inaccurate assignment of codons of transcripts.
For example, for gene uc008cjg.1, the start codon is at chr17: 35916361-35916363 while in the files mm10.codons.df and mm10.codons.bed, this chromosome location is at codon 2
$ cat mm10.codons.bed | grep 'uc008cjg.1' | head -12Another example where the codon assignments are entirely different from the reference is uc007vnb.1. The start codon is at chr15:37003817-37003820 but the codon file has very different annotations.
$cat mm10.codons.bed | grep 'uc007vnb.1' | head -20Assuming that codon 0 is the start codon in this file, I found that only 3380(7%) of 46355 transcripts have ATG as start codon
cat mm10.codons.bed | awk '{if($5==0)print $5,$7}' | sort | uniq -cI hope this bug can be fixed so that scikit-ribo can be run on mm10 data.
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